Show complete data for human cells assay. The location(s) are highlighted in the illustration on the right.

Localized to the nucleoplasm. In addition localized to the cytosol.

RNA cell categoryi

The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all TPM values in all analyzed cell lines.

Protein evidence scores are generated from several independent sources and are classified as evidence at i) protein level, ii) transcript level, iii) no evidence, or iv) not available.

Evidence at protein level

Main locationi

The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations. It is highlighted in the illustration to the right. If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively.

Localized to the Nucleoplasm

Additional locationi

Additional locations are characterized by either a markedly lower staining intensity than the main location, or that it is only observed in a subset of the cell lines. They are highlighted in the illustration to the right. If available, links to overrepresentation analyses in Reactome, a free, open-source, curated and peer reviewed biological pathway database, are provided. An analysis is done for the corresponding gene set of the proteome localizing to the main and additional locations of the protein on this page, respectively.

The location(s) are validated based on analysis of GFP-tagged protein.

DATA RELIABILITY

Reliability scorei

A reliability score is set for all genes and indicates the level of reliability of the analyzed protein expression pattern based on available protein/RNA/gene characterization data. The reliability of the annotated protein expression data is also scored depending on similarity in immunostaining patterns and consistency with available experimental gene/protein characterization data in the UniProtKB/Swiss-Prot database.

Below is an overview of RNA expression data generated in the HPA project. The analyzed cell lines are divided into 12 color-coded groups according to the organ they were obtained from. By clicking the toolbars in the top right corner it is possible to sort the cell lines in the chart by different criteria: the organ and the origin that the cell line was obtained from, the category of the cell line according to cellosaurus, alphabetically or by descending RNA expression. Detailed information about a specific cell line can be accessed by hovering over the corresponding bar in the chart. The RNA-sequencing results generated in the HPA are reported as number of Transcripts per Kilobase Million (TPM). In the Human Protein Atlas a TPM value of 1.0 is defined as a treshhold for expression of the corresponding protein.

The cell lines in the Human Protein Atlas have been analyzed by RNA-seq to estimate the transcript abundance of each protein-coding gene. The RNA-seq data was then used to classify all genes according to their cell line-specific expression into one of six different categories, defined based on the total set of all TPM values in all analyzed cell lines.

Cell lines sorted after the cell line category according to Cellosaurus.

Cell lines sorted on descending RNA expression.

Cell lines sorted alphabetically.

HUMAN CELLSi

The "human cells" section gives an overview about the subcellular location of the protein of interest obtained by indirect immunofluorescence microscopy, an antibody-based protein-visualization technique. The immunofluorescent analysis is carried out in three different cell lines, one of them always being U-2 OS. A selection of immunofluorescent images is displayed below. Three different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The HPA-antibody staining targeting the protein of interest is shown in green. To change which images to compare, use the checkboxes next to the images at the bottom. Three images can be compared at a time. All images are clickable for an enlarged view. The selected image will appear in large size and miniature images with all other staining results for this gene will be listed at the top left of the image. The selected miniature image has an orange overlay. For cell structure reference, visit the cell dictionary.

Summaryi

Summary of the immunofluorescent analysis in all studied cell lines with all tested antibodies.

Localized to the nucleoplasm. In addition localized to the cytosol.

Main locationi

The main location is characterized by presence in all tested cell lines and/or increased intensity compared to other locations.

Nucleoplasm

Additional locationi

Additional locations are characterized by either a markedly lower staining intensity than the main location, or that it is only observed in a subset of the cell lines.

Cytosol

Toggle channelsi

Three different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue, microtubules in red and ER in yellow. The HPA-antibody staining targeting the protein of interest is shown in green. By using the "toggle channels"-buttons, the different channels can be turned on and off. The intensity toggle shows the pixel intensity range in 16 different colors for the selected channel. The object toggle shows the computational segmentation of the cells used for further analysis in the HPA project. For samples where cell cycle dependency for the protein is suggested according to a correlation assay the predicted cell cycle position of each cell is displayed when using the object toggle.

Low

High

G1

S

G2

M

N/A

Thumbnaili

Representative images for the assay. Three images can be compared at the same time. To change which images to compare, use the checkboxes next to the images below. All images are clickable for an enlarged view. The selected image will appear in large size and miniature images with all other staining results for this gene will be listed at the top left of the image. The selected miniature image has an orange overlay.

Antibodyi

Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.

As the images in the Cell Atlas provide single cell resolution, variations in protein expression patterns from cell to cell can be observed. A cell-to-cell variation can either be observed in the intensity of the immunofluorescent signal or in the spatial distribution pattern of the protein. This column contains information about whether and for which of the annotated locations a cell-to-cell variation pattern was manually annotated.

The GFP section gives an overview of the colocalization of one or more antibodies with GFP-tagged target protein in HeLa cells. Read more about antibody validation by GFP colocalization. At the top of this section a selected image for each antibody is shown together with a validation summary for the antibody. A selection of immunofluorescent images using the antibody in cells expressing GFP-tagged target proteins as well as in untransfected HeLa cells is displayed below. The antibody staining, GFP and two organelle probes are displayed as different channels in the multicolor images. By using the "toggle channels"-buttons, the different channels can be turned on and off. To change which images to compare, use the checkboxes next to the images at the bottom. Three images can be compared at a time. All images are clickable for an enlarged view. The selected image will appear in large size and miniature images with all other staining results for this gene will be listed at the top left of the image. The selected miniature image has an orange overlay. For cell structure reference, visit the cell dictionary.

Antibodyi

Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.

Summary of the GFP validation assay. Antibodies are analyzed in HeLa cell lines stably expressing GFP-tagged target protein. The target protein can be tagged at either the N- or C-terminal end of the target gene; for some genes both versions are available. Read more about the used BAC cell line by clicking the BAC cell line ID which links to the BaCe Bank, an open BAC and CellLine database created by the Hyman lab, the suppliers of the BAC cell lines. For each GFP validation assay a validation score is assigned based on colocalization of the antibody staining and the GFP-tagged protein.

Two different organelle probes are displayed as different channels in the multicolor images - nucleus stained in blue and microtubules in red. The HPA-antibody staining targeting the protein of interest is shown in green and the staining of the GFP-tagged protein in purple. By using the "toggle channels"-buttons, the different channels can be turned on and off. The intensity toggle shows the pixel intensity range in 16 different colors for the selected channel.

Low

High

G1

S

G2

M

N/A

Thumbnaili

Representative images for the assay. Three images can be compared at the same time. To change which images to compare, use the checkboxes next to the images below. All images are clickable for an enlarged view. The selected image will appear in large size and miniature images with all other staining results for this gene will be listed at the top left of the image. The selected miniature image has an orange overlay.

Antibodyi

Antibody used for analysis. Clicking the antibody ID links to the antibody validation page.

Read more about the used BAC cell line by clicking the BAC cell line ID which links to the BaCe Bank, an open BAC and CellLine database created by the Hyman lab, the suppliers of the BAC cell lines. The untransfected HeLa control cells are referred to as "normal".

Tagi

The GFP construct can be tagged to the target protein at either the N- or C-terminal, for some genes both versions are available.

Gene information from Ensembl and Entrez, as well as links to available gene identifiers are displayed here. Information was retrieved from Ensembl if not indicated otherwise.

Gene name

PPP2R4 (HGNC Symbol)

Synonyms

PR53, PTPA

Description

Protein phosphatase 2A activator, regulatory subunit 4 (HGNC Symbol)

Entrez gene summary

Protein phosphatase 2A is one of the four major Ser/Thr phosphatases and is implicated in the negative control of cell growth and division. Protein phosphatase 2A holoenzymes are heterotrimeric proteins composed of a structural subunit A, a catalytic subunit C, and a regulatory subunit B. The regulatory subunit is encoded by a diverse set of genes that have been grouped into the B/PR55, B'/PR61, and B''/PR72 families. These different regulatory subunits confer distinct enzymatic specificities and intracellular localizations to the holozenzyme. The product of this gene belongs to the B' family. This gene encodes a specific phosphotyrosyl phosphatase activator of the dimeric form of protein phosphatase 2A. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

The protein browser displays the antigen location on the target protein(s) and the features of the target protein. The tabs at the top of the protein view section can be used to switch between the different splice variants to which an antigen has been mapped.

At the top of the view, the position of the antigen (identified by the corresponding HPA identifier) is shown as a green bar. A yellow triangle on the bar indicates a <100% sequence identity to the protein target.

Under the antigens, the maximum percent sequence identity of the protein to all other proteins from other human genes is displayed, using a sliding window of 10 aa residues (HsID 10) or 50 aa residues (HsID 50) (read more).

If a signal peptide is predicted by a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius (turquoise) and/or transmembrane regions (orange) are predicted by MDM, these are displayed.

Low complexity regions are shown in yellow and InterPro regions in green. Common (purple) and unique (grey) regions between different splice variants of the gene are also displayed (read more), and at the bottom of the protein view is the protein scale.

The protein information section displays alternative protein-coding transcripts (splice variants) encoded by this gene according to the Ensembl database.

The ENSP identifier links to the Ensembl website protein summary, while the ENST identifier links to the Ensembl website transcript summary for the selected splice variant. The data in the UniProt column can be expanded to show links to all matching UniProt identifiers for this protein.

The protein classes assigned to this protein are shown if expanding the data in the protein class column. Parent protein classes are in bold font and subclasses are listed under the parent class.

The Gene Ontology terms assigned to this protein are listed if expanding the Gene ontology column. The length of the protein (amino acid residues according to Ensembl), molecular mass (kDalton), predicted signal peptide (according to a majority of the signal peptide predictors SPOCTOPUS, SignalP 4.0, and Phobius) and the number of predicted transmembrane region(s) (according to MDM) are also reported.